Align ABC transporter ATP-binding protein (characterized, see rationale)
to candidate 6937828 Sama_1969 ABC transporter, ATP-binding protein (RefSeq)
Query= uniprot:A0A165KC86 (260 letters) >FitnessBrowser__SB2B:6937828 Length = 301 Score = 107 bits (268), Expect = 2e-28 Identities = 72/220 (32%), Positives = 114/220 (51%), Gaps = 20/220 (9%) Query: 15 ISKRFGGLQALSDVGITIKRGQVYGLIGPNGAGKTTFFNVITGLYTPDAGTFELAGKPYE 74 ++KR+G AL DV + ++ G L+GPNGAGKTT +++ G PD G+ E+ G + Sbjct: 9 LTKRYGSKTALDDVSLQVEAGAPVALVGPNGAGKTTLMSLMCGYIQPDGGSLEILG--HV 66 Query: 75 PTAVHEVAKAGIARTFQNIRLFAEMTALENVMVGRHIRTGSGLFGAVFRTKGFKAEEAAI 134 P + + K L + N VG + + L +GF A++A Sbjct: 67 PGSRQLLGKV--------CALPQDALLDPNFSVGEQLSFFASL-------QGFSAKDA-- 109 Query: 135 AKRAQELLDYVGIGKFADYKARTLSYGDQRRLEIARALATDPQLIALDEPAAGMNATEKV 194 + A+ +L+ V + A +K LS+G +R+ IA+AL PQL+ LDEP AG++ Sbjct: 110 RREAERVLELVELKDAARHKPTALSHGMGKRVAIAQALIGTPQLVLLDEPTAGLDPANAR 169 Query: 195 QLRELIDRIRNDNRTILLIEHDVKLVMGLCDRVTVLDYGK 234 +RELI ++ T L+ H+++ + LCD V LD GK Sbjct: 170 AVRELISH-ASEQTTFLISSHNLEELERLCDTVLYLDKGK 208 Lambda K H 0.319 0.137 0.384 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 185 Number of extensions: 5 Number of successful extensions: 2 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 260 Length of database: 301 Length adjustment: 26 Effective length of query: 234 Effective length of database: 275 Effective search space: 64350 Effective search space used: 64350 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 47 (22.7 bits)
This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory